How to rearrange gene ontology obo file?

Question

I have a gene ontology obo file, and would like to rearrange the obo format file in a single column to a text file in three columns comprised of 'parent (id:GO:xxxxxxx)', 'child (is_a: GO:xxxxxxx, part_of GO:xxxxxxx, or positively/negatively_regulates GO:xxxxxxx. For example...

Thank you for your help in advance!

Original file:

[Term]
id: GO:0000001 # parent
name: mitochondrion inheritance
namespace: biological_process
def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
synonym: "mitochondrial inheritance" EXACT []
is_a: GO:0048308 ! organelle inheritance # child
is_a: GO:0048311 ! mitochondrion distribution # child

[Term]
id: GO:0000015 # parent
name: phosphopyruvate hydratase complex
namespace: cellular_component
def: "A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water." [GOC:jl, ISBN:0198506732]
subset: goslim_metagenomics
synonym: "enolase complex" EXACT []
is_a: GO:1902494 ! catalytic complex # child
relationship: part_of GO:0005829 ! cytosol # child

[Term]
id: GO:0000122 # parent
name: negative regulation of transcription by RNA polymerase II
namespace: biological_process
alt_id: GO:0010553
alt_id: GO:0045816
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:go_curators, GOC:txnOH]
synonym: "down regulation of global transcription from RNA polymerase II promoter" RELATED []
synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "down-regulation of global transcription from RNA polymerase II promoter" RELATED []
synonym: "down-regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "downregulation of global transcription from RNA polymerase II promoter" RELATED []
synonym: "downregulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "inhibition of global transcription from RNA polymerase II promoter" RELATED []
synonym: "inhibition of transcription from RNA polymerase II promoter" EXACT []
synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter" RELATED []
synonym: "negative regulation of global transcription from Pol II promoter" RELATED []
synonym: "negative regulation of transcription from Pol II promoter" EXACT []
synonym: "negative regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "negative regulation of transcription from RNA polymerase II promoter, global" RELATED []
is_a: GO:0006357 ! regulation of transcription by RNA polymerase II # child
is_a: GO:0045892 ! negative regulation of DNA-templated transcription # child
relationship: negatively_regulates GO:0006366 ! transcription by RNA polymerase II # child

Desired format:

Parent       Child       Relationship
GO:0000001   GO:0048308  is_a
GO:0000001   GO:0048311  is_a
GO:0000015   GO:1902494  is_a
GO:0000015   GO:0005829  part_of
GO:0000122   GO:0006357  is_a
GO:0000122   GO:0045892  is_a
GO:0000122   GO:0006366  negatively_regulates

Answer 1

One potential solution using awk:

awk 'BEGIN {
    OFS = "\t"
    print "Parent", "Child", "Relationship"
}

/GO:[[:digit:]]{1,}/ {
    if ($1 ~ /^id:/) {
    parent_id = $2
} else if ($1 ~ /^is_a:/) {
        gsub(":", "", $1)
    print parent_id, $2, $1
} else if ($1 ~ /^relationship:/) {
        print parent_id, $3, $2
    }
}' test.txt
Parent      Child       Relationship
GO:0000001  GO:0048308  is_a
GO:0000001  GO:0048311  is_a
GO:0000015  GO:1902494  is_a
GO:0000015  GO:0005829  part_of
GO:0000122  GO:0006357  is_a
GO:0000122  GO:0045892  is_a
GO:0000122  GO:0006366  negatively_regulates

---

Including comments:

awk 'BEGIN {                      # before processing the first line
    OFS = "\t"                    # set the output field separator to tab
    print "Parent", "Child", "Relationship"    # and print the header
}

/GO:[[:digit:]]{1,}/ {    # for any line that contains a GO term
    if ($1 ~ /^id:/) {            # if the line starts with id:
    parent_id = $1                # set the parent id
} else if ($1 ~ /^is_a/) {        # then, for lines that start with is_a 
        gsub(":", "", $1)         # remove the colon
    print parent_id, $2, $1       # and print the parent, child and relationship
} else if ($1 ~ /^relationship:/) {  # then, for lines that start with relationship
        print parent_id, $3, $2   # print the parent, child, and relationship
    }
}' test.txt